GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Herbaspirillum seropedicae SmR1

Align dihydrolipoyl dehydrogenase; EC 1.8.1.4 (characterized)
to candidate HSERO_RS16580 HSERO_RS16580 glutathione reductase

Query= CharProtDB::CH_123536
         (491 letters)



>FitnessBrowser__HerbieS:HSERO_RS16580
          Length = 458

 Score =  230 bits (586), Expect = 9e-65
 Identities = 150/457 (32%), Positives = 232/457 (50%), Gaps = 17/457 (3%)

Query: 26  YDVVVIGGGPGGYVAAIKAAQLGLNTACIEKRGALGGTCLNVGCIPSKSLLNNSHLLHQI 85
           YD+  IGGG GG  AA  A+Q G      EK G LGGTC+N+GCIP K +  ++H  H+ 
Sbjct: 6   YDLFTIGGGSGGVRAARFASQAGARVGLAEK-GDLGGTCVNLGCIPKKLMSYSAHY-HEE 63

Query: 86  QHEAKERGISIQGEVGVDFPKLMAAKEKAVKQLTGGIEMLFKKNKVDYLKGAGSFVNEKT 145
             +A   G ++ G+   D+  LMA K++ +  L      L    KV   +G     +  T
Sbjct: 64  FADAAGYGWTLNGQPSFDWSALMANKDREIAHLNDIYLRLLDNAKVSLHRGFAKVEDAHT 123

Query: 146 VKVTPIDGSEAQEVEADHIIVATGSEPTP--FPGIEIDEERIVTSTGILSLKEVPERLAI 203
           V V      + Q   A HI+VATG  P     PG E+     +TS     LK +P+R  +
Sbjct: 124 VNV------DGQRFTARHILVATGGRPDKPAIPGAELG----ITSDDFFHLKALPQRAVV 173

Query: 204 IGGGIIGLEMASVYARLGSKVTVIEFQNAIGAGMDAEVAKQSQKLLAKQGLD--FKLGTK 261
           +GGG I +E+AS+   LG +VT++  +  +   MDA++       +AK+G+   F    +
Sbjct: 174 LGGGYIAVELASILNGLGCEVTLVYRRERLLRNMDADLGIHLADEMAKKGIRIVFNASIE 233

Query: 262 VVKGERDGEVVKIEVEDVKSGKKSDLEADVLLVAIGRRPFTEGLNFEAIGLEKDNKGRLI 321
            ++ E+ GE  +  V+ V+      L A  +L A GR   T GL  +  G++    G + 
Sbjct: 234 AIEAEQAGEASEASVKTVRLTNGEALSAQCVLFATGRTANTAGLGLQEAGVKLKANGAIE 293

Query: 322 IDDQFKTKHDHIRVIGDVTFGPMLAHKAEEEGIAAAEYI-KKGHGHVNYANIPSVMYTHP 380
           ++  F++    I  +GDV     L   A  E +A    +  KG   ++YANIP+ +++HP
Sbjct: 294 VNQDFESSVPSILAVGDVIDRVALTPVALAEAMAVVSRLFGKGERGMSYANIPTAVFSHP 353

Query: 381 EVAWVGLNEEQLKEQGIKYKVGKFPFIANSRAKTNMDTDGFVKFIADAETQRVLGVHIIG 440
            V  VGL+EE+ ++Q  + ++ K  F       +      F+K + DA T RVLGVH++G
Sbjct: 354 NVGTVGLSEEEARQQFGELRIFKTDFKPLKNTLSRNTERTFMKLVVDARTDRVLGVHMVG 413

Query: 441 PNAGEMIAEAGLALEYGASTEDISRTCHAHPTLSEAF 477
            +AGE+I    +AL+ GA+      T   HPT +E F
Sbjct: 414 GDAGEVIQGFAVALQCGATKAQFDTTIGIHPTSAEEF 450


Lambda     K      H
   0.316    0.135    0.381 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 460
Number of extensions: 28
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 491
Length of database: 458
Length adjustment: 33
Effective length of query: 458
Effective length of database: 425
Effective search space:   194650
Effective search space used:   194650
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory